Mercurial > repos > iuc > goseq
diff goseq.xml @ 9:ef2ad746b589 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e230a8db9e090c6e0ea9577863ec6153df79e145"
author | iuc |
---|---|
date | Sun, 06 Jun 2021 22:47:36 +0000 |
parents | 8b3e3657034e |
children | 43798b4caee0 |
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--- a/goseq.xml Fri Sep 06 07:50:46 2019 -0400 +++ b/goseq.xml Sun Jun 06 22:47:36 2021 +0000 @@ -1,18 +1,27 @@ <tool id="goseq" name="goseq" version="@VERSION@+@GALAXY_VERSION@"> <description>tests for overrepresented gene categories</description> + <xrefs> + <xref type="bio.tools">goseq</xref> + </xrefs> + <edam_topics> + <edam_topic>topic_3308</edam_topic> + </edam_topics> + <edam_operations> + <edam_operation>operation_2436</edam_operation> + </edam_operations> <macros> - <token name="@VERSION@">1.36.0</token> + <token name="@VERSION@">1.44.0</token> <token name="@GALAXY_VERSION@">galaxy0</token> </macros> <requirements> <requirement type="package" version="@VERSION@">bioconductor-goseq</requirement> - <requirement type="package" version="3.8.2">bioconductor-org.hs.eg.db</requirement> - <requirement type="package" version="3.8.2">bioconductor-org.dm.eg.db</requirement> - <requirement type="package" version="3.8.2">bioconductor-org.dr.eg.db</requirement> - <requirement type="package" version="3.8.2">bioconductor-org.mm.eg.db</requirement> - <requirement type="package" version="0.8.3">r-dplyr</requirement> - <requirement type="package" version="3.2.1">r-ggplot2</requirement> - <requirement type="package" version="1.6.2">r-optparse</requirement> + <requirement type="package" version="3.13.0">bioconductor-org.hs.eg.db</requirement> + <requirement type="package" version="3.13.0">bioconductor-org.dm.eg.db</requirement> + <requirement type="package" version="3.13.0">bioconductor-org.dr.eg.db</requirement> + <requirement type="package" version="3.13.0">bioconductor-org.mm.eg.db</requirement> + <requirement type="package" version="1.0.6">r-dplyr</requirement> + <requirement type="package" version="3.3.3">r-ggplot2</requirement> + <requirement type="package" version="1.6.6">r-optparse</requirement> </requirements> <stdio> <regex match="Execution halted" @@ -194,7 +203,7 @@ <output name="top_plot" ftype="pdf" file="topgo.pdf" compare="sim_size"/> <output name="wallenius_tab"> <assert_contents> - <has_text_matching expression="category.*over_represented_pvalue.*under_represented_pvalue.*numDEInCat.*numInCat.*term.*ontology.*p.adjust.over_represented.*p.adjust.under_represented" /> + <has_text_matching expression="category.*over_represented_pvalue.*under_represented_pvalue.*numDEInCat.*numInCat.*term.*ontology.*p_adjust_over_represented.*p_adjust_under_represented" /> <has_text_matching expression="GO:0000278.*0.01" /> </assert_contents> </output> @@ -226,13 +235,13 @@ </section> <output name="wallenius_tab"> <assert_contents> - <has_text_matching expression="category.*over_represented_pvalue.*under_represented_pvalue.*numDEInCat.*numInCat.*term.*ontology.*p.adjust.over_represented.*p.adjust.under_represented" /> - <has_text_matching expression="GO:0005576.*9.0" /> + <has_text_matching expression="category.*over_represented_pvalue.*under_represented_pvalue.*numDEInCat.*numInCat.*term.*ontology.*p_adjust_over_represented.*p_adjust_under_represented" /> + <has_text_matching expression="GO:0005576.*0.9" /> </assert_contents> </output> <output name="cat_genes_tab"> <assert_contents> - <has_text_matching expression="Categories.*DEgenes" /> + <has_text_matching expression="category.*de_genes" /> <has_text_matching expression="GO:0005615.*ENSG00000090402,ENSG00000108953,ENSG00000070961" /> </assert_contents> </output> @@ -264,8 +273,8 @@ </section> <output name="wallenius_tab"> <assert_contents> - <has_text_matching expression="category.*over_represented_pvalue.*under_represented_pvalue.*numDEInCat.*numInCat.*term.*ontology.*p.adjust.over_represented.*p.adjust.under_represented" /> - <has_text_matching expression="GO:0016569.*0.8" /> + <has_text_matching expression="category.*over_represented_pvalue.*under_represented_pvalue.*numDEInCat.*numInCat.*term.*ontology.*p_adjust_over_represented.*p_adjust_under_represented" /> + <has_text_matching expression="GO:0016569.*0.90" /> </assert_contents> </output> </test> @@ -438,7 +447,7 @@ Example: =========== =============== ================ ============ ========== ======================================== ========== =================== ==================== -*category* *over_rep_pval* *under_rep_pval* *numDEInCat* *numInCat* *term* *ontology* *p.adjust.over_rep* *p.adjust.under_rep* +*category* *over_rep_pval* *under_rep_pval* *numDEInCat* *numInCat* *term* *ontology* *p_adjust_over_rep* *p_adjust_under_rep* ----------- --------------- ---------------- ------------ ---------- ---------------------------------------- ---------- ------------------- -------------------- GO\:0005576 0.000054 0.999975 56 142 extracellular region CC 0.394825 1 GO\:0005840 0.000143 0.999988 9 12 ribosome CC 0.394825 1